## Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
##   object 'config' not found

Project info

Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)

Normalization: Viral read count

TES dynamics

Those reads were counted only, where the 3-prime adapters were “correct” (according to LoRTIA)

Statistics of counts

Difference from mean

Varcoeff

Clustering of samples

## Bootstrap (r = 0.49)... Done.
## Bootstrap (r = 0.6)... Done.
## Bootstrap (r = 0.68)... Done.
## Bootstrap (r = 0.79)... Done.
## Bootstrap (r = 0.89)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.09)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.3)... Done.
## Bootstrap (r = 1.38)... Done.

The sample 48h_3 stands out!

Filtering of samples

Clustering of genes into de-novo clusters using hierarchial clustering

Cluster memberships

## Bootstrap (r = 0.5)... Done.
## Bootstrap (r = 0.58)... Done.
## Bootstrap (r = 0.69)... Done.
## Bootstrap (r = 0.77)... Done.
## Bootstrap (r = 0.88)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.08)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.27)... Done.
## Bootstrap (r = 1.38)... Done.

Optimal number of clusters

Find the optimal number of clusters to cut the tree at and calculate

Clustering statistics: Cluster number: 5

## Key: <cluster>
##     cluster                          gene        si        au        bp
##       <int>                        <char>     <num>     <num>     <num>
##  1:       1                          ORF1 1.0000000 1.0000000 1.0000000
##  2:       1            ORF7,  ORF6,  ORF5 1.0000000 1.0000000 1.0000000
##  3:       1                  ORF10, ORF11 1.0000000 1.0000000 1.0000000
##  4:       1                         ORF17 1.0000000 1.0000000 1.0000000
##  5:       1           ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
##  6:       1                         ORF30 1.0000000 1.0000000 1.0000000
##  7:       1                         ORF31 1.0000000 1.0000000 1.0000000
##  8:       1           ORF32, ORF33, ORF34 1.0000000 1.0000000 1.0000000
##  9:       1                         ORF63 1.0000000 1.0000000 1.0000000
## 10:       1                        NOIR_1 1.0000000 1.0000000 1.0000000
## 11:       1                       ORF65_1 1.0000000 1.0000000 1.0000000
## 12:       1                ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
## 13:       1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
## 14:       1                        NOIR_2 1.0000000 1.0000000 1.0000000
## 15:       2                          ORF2 0.9984163 0.9994835 0.9913488
## 16:       2                          ORF3 0.9984163 0.9994835 0.9913488
## 17:       2                          ORF8 0.9984163 0.9994835 0.9913488
## 18:       2                          ORF9 0.9984163 0.9994835 0.9913488
## 19:       2           ORF12, ORF13, ORF14 0.9984163 0.9994835 0.9913488
## 20:       2                         ORF18 0.9984163 0.9994835 0.9913488
## 21:       2                         ORF22 0.9984163 0.9994835 0.9913488
## 22:       2                         ORF23 0.9984163 0.9994835 0.9913488
## 23:       2           ORF27, ORF26, ORF25 0.9984163 0.9994835 0.9913488
## 24:       2                  ORF28, ORF29 0.9984163 0.9994835 0.9913488
## 25:       2  ORF37, ORF36, ORF35, ORF35.5 0.9984163 0.9994835 0.9913488
## 26:       2                         ORF36 0.9984163 0.9994835 0.9913488
## 27:       2                         ORF37 0.9984163 0.9994835 0.9913488
## 28:       2                         ORF38 0.9984163 0.9994835 0.9913488
## 29:       2                           CTO 0.9984163 0.9994835 0.9913488
## 30:       2                         ORF40 0.9984163 0.9994835 0.9913488
## 31:       2            ORF41, ORF42, OF43 0.9984163 0.9994835 0.9913488
## 32:       2                         ORF44 0.9984163 0.9994835 0.9913488
## 33:       2    ORF48, ORF49, ORF50, ORF51 0.9984163 0.9994835 0.9913488
## 34:       2                       ORF66_1 0.9984163 0.9994835 0.9913488
## 35:       3                          ORF4 0.1234810 0.5986755 0.5152662
## 36:       3                       ORF64_1 0.1234810 0.5986755 0.5152662
## 37:       3                  ORF69, ORF70 0.1234810 0.5986755 0.5152662
## 38:       4    ORF18, ORF17, ORF16, ORF15 0.9835030 0.9950607 0.9367211
## 39:       4                         ORF19 0.9835030 0.9950607 0.9367211
## 40:       4                         ORF24 0.9835030 0.9950607 0.9367211
## 41:       4                         ORF52 0.9835030 0.9950607 0.9367211
## 42:       4                  ORF53, ORF54 0.9835030 0.9950607 0.9367211
## 43:       4                  ORF57, ORF58 0.9835030 0.9950607 0.9367211
## 44:       4     ORF62, ORF61, ORF60,ORF59 0.9835030 0.9950607 0.9367211
## 45:       4           ORF71, ORF72, ORF73 0.9835030 0.9950607 0.9367211
## 46:       5                         ORF39 0.2997682 0.6679639 0.6197278
## 47:       5                  ORF45, ORF46 0.2997682 0.6679639 0.6197278
##     cluster                          gene        si        au        bp
##           se.si        se.au       se.bp          v          c       pchi
##           <num>        <num>       <num>      <num>      <num>      <num>
##  1: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  2: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  3: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  4: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  5: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  6: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  7: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  8: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  9: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
## 10: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
## 11: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
## 12: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
## 13: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
## 14: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
## 15: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 16: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 17: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 18: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 19: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 20: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 21: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 22: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 23: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 24: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 25: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 26: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 27: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 28: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 29: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 30: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 31: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 32: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 33: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 34: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 35: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 36: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 37: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 38: 0.004356308 0.0015792923 0.002805170 -2.0539348 0.52611717 0.07101361
## 39: 0.004356308 0.0015792923 0.002805170 -2.0539348 0.52611717 0.07101361
## 40: 0.004356308 0.0015792923 0.002805170 -2.0539348 0.52611717 0.07101361
## 41: 0.004356308 0.0015792923 0.002805170 -2.0539348 0.52611717 0.07101361
## 42: 0.004356308 0.0015792923 0.002805170 -2.0539348 0.52611717 0.07101361
## 43: 0.004356308 0.0015792923 0.002805170 -2.0539348 0.52611717 0.07101361
## 44: 0.004356308 0.0015792923 0.002805170 -2.0539348 0.52611717 0.07101361
## 45: 0.004356308 0.0015792923 0.002805170 -2.0539348 0.52611717 0.07101361
## 46: 0.038198268 0.0281444577 0.005132608 -0.3695320 0.06476593 0.63603543
## 47: 0.038198268 0.0281444577 0.005132608 -0.3695320 0.06476593 0.63603543
##           se.si        se.au       se.bp          v          c       pchi

## [1] "ORF27, ORF26, ORF25"          "ORF37, ORF36, ORF35, ORF35.5"
## [3] "ORF41, ORF42, OF43"           "ORF24"
## [1] 4
## [1] "ORF4"         "ORF64_1"      "ORF69, ORF70" "ORF39"        "ORF45, ORF46"
## [1] 5

Clustering statistics: Cluster number: 6

## Key: <cluster>
##     cluster                          gene        si        au        bp
##       <int>                        <char>     <num>     <num>     <num>
##  1:       1                          ORF1 1.0000000 1.0000000 1.0000000
##  2:       1            ORF7,  ORF6,  ORF5 1.0000000 1.0000000 1.0000000
##  3:       1                  ORF10, ORF11 1.0000000 1.0000000 1.0000000
##  4:       1                         ORF17 1.0000000 1.0000000 1.0000000
##  5:       1           ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
##  6:       1                         ORF30 1.0000000 1.0000000 1.0000000
##  7:       1                         ORF31 1.0000000 1.0000000 1.0000000
##  8:       1           ORF32, ORF33, ORF34 1.0000000 1.0000000 1.0000000
##  9:       1                         ORF63 1.0000000 1.0000000 1.0000000
## 10:       1                        NOIR_1 1.0000000 1.0000000 1.0000000
## 11:       1                       ORF65_1 1.0000000 1.0000000 1.0000000
## 12:       1                ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
## 13:       1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
## 14:       1                        NOIR_2 1.0000000 1.0000000 1.0000000
## 15:       2                          ORF2 0.9984163 0.9994835 0.9913488
## 16:       2                          ORF3 0.9984163 0.9994835 0.9913488
## 17:       2                          ORF8 0.9984163 0.9994835 0.9913488
## 18:       2                          ORF9 0.9984163 0.9994835 0.9913488
## 19:       2           ORF12, ORF13, ORF14 0.9984163 0.9994835 0.9913488
## 20:       2                         ORF18 0.9984163 0.9994835 0.9913488
## 21:       2                         ORF22 0.9984163 0.9994835 0.9913488
## 22:       2                         ORF23 0.9984163 0.9994835 0.9913488
## 23:       2           ORF27, ORF26, ORF25 0.9984163 0.9994835 0.9913488
## 24:       2                  ORF28, ORF29 0.9984163 0.9994835 0.9913488
## 25:       2  ORF37, ORF36, ORF35, ORF35.5 0.9984163 0.9994835 0.9913488
## 26:       2                         ORF36 0.9984163 0.9994835 0.9913488
## 27:       2                         ORF37 0.9984163 0.9994835 0.9913488
## 28:       2                         ORF38 0.9984163 0.9994835 0.9913488
## 29:       2                           CTO 0.9984163 0.9994835 0.9913488
## 30:       2                         ORF40 0.9984163 0.9994835 0.9913488
## 31:       2            ORF41, ORF42, OF43 0.9984163 0.9994835 0.9913488
## 32:       2                         ORF44 0.9984163 0.9994835 0.9913488
## 33:       2    ORF48, ORF49, ORF50, ORF51 0.9984163 0.9994835 0.9913488
## 34:       2                       ORF66_1 0.9984163 0.9994835 0.9913488
## 35:       3                          ORF4 0.1234810 0.5986755 0.5152662
## 36:       3                  ORF69, ORF70 0.1234810 0.5986755 0.5152662
## 37:       4    ORF18, ORF17, ORF16, ORF15 0.9835030 0.9950607 0.9367211
## 38:       4                         ORF19 0.9835030 0.9950607 0.9367211
## 39:       4                         ORF24 0.9835030 0.9950607 0.9367211
## 40:       4                         ORF52 0.9835030 0.9950607 0.9367211
## 41:       4                  ORF53, ORF54 0.9835030 0.9950607 0.9367211
## 42:       4                  ORF57, ORF58 0.9835030 0.9950607 0.9367211
## 43:       4     ORF62, ORF61, ORF60,ORF59 0.9835030 0.9950607 0.9367211
## 44:       4           ORF71, ORF72, ORF73 0.9835030 0.9950607 0.9367211
## 45:       5                         ORF39 0.2997682 0.6679639 0.6197278
## 46:       5                  ORF45, ORF46 0.2997682 0.6679639 0.6197278
## 47:       6                       ORF64_1 0.8300888 0.9339235 0.8267064
##     cluster                          gene        si        au        bp
##           se.si        se.au       se.bp          v          c       pchi
##           <num>        <num>       <num>      <num>      <num>      <num>
##  1: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  2: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  3: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  4: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  5: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  6: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  7: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  8: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  9: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
## 10: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
## 11: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
## 12: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
## 13: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
## 14: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
## 15: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 16: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 17: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 18: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 19: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 20: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 21: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 22: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 23: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 24: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 25: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 26: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 27: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 28: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 29: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 30: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 31: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 32: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 33: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 34: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 35: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 36: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 37: 0.004356308 0.0015792923 0.002805170 -2.0539348 0.52611717 0.07101361
## 38: 0.004356308 0.0015792923 0.002805170 -2.0539348 0.52611717 0.07101361
## 39: 0.004356308 0.0015792923 0.002805170 -2.0539348 0.52611717 0.07101361
## 40: 0.004356308 0.0015792923 0.002805170 -2.0539348 0.52611717 0.07101361
## 41: 0.004356308 0.0015792923 0.002805170 -2.0539348 0.52611717 0.07101361
## 42: 0.004356308 0.0015792923 0.002805170 -2.0539348 0.52611717 0.07101361
## 43: 0.004356308 0.0015792923 0.002805170 -2.0539348 0.52611717 0.07101361
## 44: 0.004356308 0.0015792923 0.002805170 -2.0539348 0.52611717 0.07101361
## 45: 0.038198268 0.0281444577 0.005132608 -0.3695320 0.06476593 0.63603543
## 46: 0.038198268 0.0281444577 0.005132608 -0.3695320 0.06476593 0.63603543
## 47: 0.022308499 0.0112787217 0.004124539 -1.2234480 0.28221817 0.39334222
##           se.si        se.au       se.bp          v          c       pchi

## [1] "ORF27, ORF26, ORF25"          "ORF37, ORF36, ORF35, ORF35.5"
## [3] "ORF41, ORF42, OF43"           "ORF24"
## [1] 4
## [1] "ORF4"         "ORF69, ORF70" "ORF39"        "ORF45, ORF46" "ORF64_1"
## [1] 5

Clustering statistics: Cluster number: 7

## Key: <cluster>
##     cluster                          gene        si        au        bp
##       <int>                        <char>     <num>     <num>     <num>
##  1:       1                          ORF1 1.0000000 1.0000000 1.0000000
##  2:       1            ORF7,  ORF6,  ORF5 1.0000000 1.0000000 1.0000000
##  3:       1                  ORF10, ORF11 1.0000000 1.0000000 1.0000000
##  4:       1                         ORF17 1.0000000 1.0000000 1.0000000
##  5:       1           ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
##  6:       1                         ORF30 1.0000000 1.0000000 1.0000000
##  7:       1                         ORF31 1.0000000 1.0000000 1.0000000
##  8:       1           ORF32, ORF33, ORF34 1.0000000 1.0000000 1.0000000
##  9:       1                         ORF63 1.0000000 1.0000000 1.0000000
## 10:       1                        NOIR_1 1.0000000 1.0000000 1.0000000
## 11:       1                       ORF65_1 1.0000000 1.0000000 1.0000000
## 12:       1                ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
## 13:       1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
## 14:       1                        NOIR_2 1.0000000 1.0000000 1.0000000
## 15:       2                          ORF2 0.9984163 0.9994835 0.9913488
## 16:       2                          ORF3 0.9984163 0.9994835 0.9913488
## 17:       2                          ORF8 0.9984163 0.9994835 0.9913488
## 18:       2                          ORF9 0.9984163 0.9994835 0.9913488
## 19:       2           ORF12, ORF13, ORF14 0.9984163 0.9994835 0.9913488
## 20:       2                         ORF18 0.9984163 0.9994835 0.9913488
## 21:       2                         ORF22 0.9984163 0.9994835 0.9913488
## 22:       2                         ORF23 0.9984163 0.9994835 0.9913488
## 23:       2           ORF27, ORF26, ORF25 0.9984163 0.9994835 0.9913488
## 24:       2                  ORF28, ORF29 0.9984163 0.9994835 0.9913488
## 25:       2  ORF37, ORF36, ORF35, ORF35.5 0.9984163 0.9994835 0.9913488
## 26:       2                         ORF36 0.9984163 0.9994835 0.9913488
## 27:       2                         ORF37 0.9984163 0.9994835 0.9913488
## 28:       2                         ORF38 0.9984163 0.9994835 0.9913488
## 29:       2                           CTO 0.9984163 0.9994835 0.9913488
## 30:       2                         ORF40 0.9984163 0.9994835 0.9913488
## 31:       2            ORF41, ORF42, OF43 0.9984163 0.9994835 0.9913488
## 32:       2                         ORF44 0.9984163 0.9994835 0.9913488
## 33:       2    ORF48, ORF49, ORF50, ORF51 0.9984163 0.9994835 0.9913488
## 34:       2                       ORF66_1 0.9984163 0.9994835 0.9913488
## 35:       3                          ORF4 0.1234810 0.5986755 0.5152662
## 36:       3                  ORF69, ORF70 0.1234810 0.5986755 0.5152662
## 37:       4    ORF18, ORF17, ORF16, ORF15 0.9835030 0.9950607 0.9367211
## 38:       4                         ORF19 0.9835030 0.9950607 0.9367211
## 39:       4                         ORF52 0.9835030 0.9950607 0.9367211
## 40:       4                  ORF53, ORF54 0.9835030 0.9950607 0.9367211
## 41:       4                  ORF57, ORF58 0.9835030 0.9950607 0.9367211
## 42:       4     ORF62, ORF61, ORF60,ORF59 0.9835030 0.9950607 0.9367211
## 43:       4           ORF71, ORF72, ORF73 0.9835030 0.9950607 0.9367211
## 44:       5                         ORF24 0.2997682 0.6679639 0.6197278
## 45:       6                         ORF39 0.8300888 0.9339235 0.8267064
## 46:       6                  ORF45, ORF46 0.8300888 0.9339235 0.8267064
## 47:       7                       ORF64_1 0.9933681 0.9978948 0.9720753
##     cluster                          gene        si        au        bp
##           se.si        se.au       se.bp          v          c       pchi
##           <num>        <num>       <num>      <num>      <num>      <num>
##  1: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  2: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  3: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  4: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  5: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  6: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  7: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  8: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  9: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
## 10: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
## 11: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
## 12: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
## 13: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
## 14: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
## 15: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 16: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 17: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 18: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 19: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 20: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 21: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 22: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 23: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 24: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 25: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 26: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 27: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 28: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 29: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 30: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 31: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 32: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 33: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 34: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 35: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 36: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 37: 0.004356308 0.0015792923 0.002805170 -2.0539348 0.52611717 0.07101361
## 38: 0.004356308 0.0015792923 0.002805170 -2.0539348 0.52611717 0.07101361
## 39: 0.004356308 0.0015792923 0.002805170 -2.0539348 0.52611717 0.07101361
## 40: 0.004356308 0.0015792923 0.002805170 -2.0539348 0.52611717 0.07101361
## 41: 0.004356308 0.0015792923 0.002805170 -2.0539348 0.52611717 0.07101361
## 42: 0.004356308 0.0015792923 0.002805170 -2.0539348 0.52611717 0.07101361
## 43: 0.004356308 0.0015792923 0.002805170 -2.0539348 0.52611717 0.07101361
## 44: 0.038198268 0.0281444577 0.005132608 -0.3695320 0.06476593 0.63603543
## 45: 0.022308499 0.0112787217 0.004124539 -1.2234480 0.28221817 0.39334222
## 46: 0.022308499 0.0112787217 0.004124539 -1.2234480 0.28221817 0.39334222
## 47: 0.002536253 0.0009466593 0.001993169 -2.3870795 0.47487133 0.20691421
##           se.si        se.au       se.bp          v          c       pchi

## [1] "ORF27, ORF26, ORF25"          "ORF37, ORF36, ORF35, ORF35.5"
## [3] "ORF41, ORF42, OF43"
## [1] 3
## [1] "ORF4"         "ORF69, ORF70" "ORF24"        "ORF39"        "ORF45, ORF46"
## [1] 5

Clustering statistics: Cluster number: 10

## Key: <cluster>
##     cluster                          gene        si        au        bp
##       <int>                        <char>     <num>     <num>     <num>
##  1:       1                          ORF1 1.0000000 1.0000000 1.0000000
##  2:       1                         ORF17 1.0000000 1.0000000 1.0000000
##  3:       1           ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
##  4:       1                         ORF31 1.0000000 1.0000000 1.0000000
##  5:       1                ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
##  6:       1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
##  7:       2                          ORF2 0.9984163 0.9994835 0.9913488
##  8:       2                          ORF8 0.9984163 0.9994835 0.9913488
##  9:       2           ORF12, ORF13, ORF14 0.9984163 0.9994835 0.9913488
## 10:       2                         ORF22 0.9984163 0.9994835 0.9913488
## 11:       2                         ORF23 0.9984163 0.9994835 0.9913488
## 12:       2           ORF27, ORF26, ORF25 0.9984163 0.9994835 0.9913488
## 13:       2  ORF37, ORF36, ORF35, ORF35.5 0.9984163 0.9994835 0.9913488
## 14:       2                         ORF36 0.9984163 0.9994835 0.9913488
## 15:       2                           CTO 0.9984163 0.9994835 0.9913488
## 16:       2                         ORF40 0.9984163 0.9994835 0.9913488
## 17:       2            ORF41, ORF42, OF43 0.9984163 0.9994835 0.9913488
## 18:       2                         ORF44 0.9984163 0.9994835 0.9913488
## 19:       3                          ORF3 0.1234810 0.5986755 0.5152662
## 20:       3                          ORF9 0.1234810 0.5986755 0.5152662
## 21:       3                         ORF18 0.1234810 0.5986755 0.5152662
## 22:       3                  ORF28, ORF29 0.1234810 0.5986755 0.5152662
## 23:       3                         ORF37 0.1234810 0.5986755 0.5152662
## 24:       3                         ORF38 0.1234810 0.5986755 0.5152662
## 25:       3    ORF48, ORF49, ORF50, ORF51 0.1234810 0.5986755 0.5152662
## 26:       3                       ORF66_1 0.1234810 0.5986755 0.5152662
## 27:       4                          ORF4 0.9835030 0.9950607 0.9367211
## 28:       4                  ORF69, ORF70 0.9835030 0.9950607 0.9367211
## 29:       5            ORF7,  ORF6,  ORF5 0.2997682 0.6679639 0.6197278
## 30:       5                         ORF30 0.2997682 0.6679639 0.6197278
## 31:       5                         ORF63 0.2997682 0.6679639 0.6197278
## 32:       5                       ORF65_1 0.2997682 0.6679639 0.6197278
## 33:       6                  ORF10, ORF11 0.8300888 0.9339235 0.8267064
## 34:       6           ORF32, ORF33, ORF34 0.8300888 0.9339235 0.8267064
## 35:       6                        NOIR_1 0.8300888 0.9339235 0.8267064
## 36:       6                        NOIR_2 0.8300888 0.9339235 0.8267064
## 37:       7    ORF18, ORF17, ORF16, ORF15 0.9933681 0.9978948 0.9720753
## 38:       7                         ORF19 0.9933681 0.9978948 0.9720753
## 39:       7                         ORF52 0.9933681 0.9978948 0.9720753
## 40:       7                  ORF53, ORF54 0.9933681 0.9978948 0.9720753
## 41:       7                  ORF57, ORF58 0.9933681 0.9978948 0.9720753
## 42:       7     ORF62, ORF61, ORF60,ORF59 0.9933681 0.9978948 0.9720753
## 43:       7           ORF71, ORF72, ORF73 0.9933681 0.9978948 0.9720753
## 44:       8                         ORF24 0.6634756 0.9263861 0.4587966
## 45:       9                         ORF39 0.9969977 0.9993334 0.9533299
## 46:       9                  ORF45, ORF46 0.9969977 0.9993334 0.9533299
## 47:      10                       ORF64_1 0.1972185 0.6641499 0.5046373
##     cluster                          gene        si        au        bp
##           se.si        se.au       se.bp          v          c       pchi
##           <num>        <num>       <num>      <num>      <num>      <num>
##  1: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  2: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  3: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  4: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  5: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  6: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  7: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
##  8: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
##  9: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 10: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 11: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 12: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 13: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 14: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 15: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 16: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 17: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 18: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
## 19: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 20: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 21: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 22: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 23: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 24: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 25: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 26: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 27: 0.004356308 0.0015792923 0.002805170 -2.0539348 0.52611717 0.07101361
## 28: 0.004356308 0.0015792923 0.002805170 -2.0539348 0.52611717 0.07101361
## 29: 0.038198268 0.0281444577 0.005132608 -0.3695320 0.06476593 0.63603543
## 30: 0.038198268 0.0281444577 0.005132608 -0.3695320 0.06476593 0.63603543
## 31: 0.038198268 0.0281444577 0.005132608 -0.3695320 0.06476593 0.63603543
## 32: 0.038198268 0.0281444577 0.005132608 -0.3695320 0.06476593 0.63603543
## 33: 0.022308499 0.0112787217 0.004124539 -1.2234480 0.28221817 0.39334222
## 34: 0.022308499 0.0112787217 0.004124539 -1.2234480 0.28221817 0.39334222
## 35: 0.022308499 0.0112787217 0.004124539 -1.2234480 0.28221817 0.39334222
## 36: 0.022308499 0.0112787217 0.004124539 -1.2234480 0.28221817 0.39334222
## 37: 0.002536253 0.0009466593 0.001993169 -2.3870795 0.47487133 0.20691421
## 38: 0.002536253 0.0009466593 0.001993169 -2.3870795 0.47487133 0.20691421
## 39: 0.002536253 0.0009466593 0.001993169 -2.3870795 0.47487133 0.20691421
## 40: 0.002536253 0.0009466593 0.001993169 -2.3870795 0.47487133 0.20691421
## 41: 0.002536253 0.0009466593 0.001993169 -2.3870795 0.47487133 0.20691421
## 42: 0.002536253 0.0009466593 0.001993169 -2.3870795 0.47487133 0.20691421
## 43: 0.002536253 0.0009466593 0.001993169 -2.3870795 0.47487133 0.20691421
## 44: 0.033546589 0.0110144449 0.005278204 -0.6729635 0.77642943 0.44948901
## 45: 0.001063096 0.0002821407 0.002535222 -2.4433858 0.76535080 0.33851817
## 46: 0.001063096 0.0002821407 0.002535222 -2.4433858 0.76535080 0.33851817
## 47: 0.040087721 0.0279291195 0.005273401 -0.2177200 0.20609572 0.79095438
##           se.si        se.au       se.bp          v          c       pchi

## character(0)
## [1] 0
##  [1] "ORF3"                       "ORF9"                      
##  [3] "ORF18"                      "ORF28, ORF29"              
##  [5] "ORF37"                      "ORF38"                     
##  [7] "ORF48, ORF49, ORF50, ORF51" "ORF66_1"                   
##  [9] "ORF7,  ORF6,  ORF5"         "ORF30"                     
## [11] "ORF63"                      "ORF65_1"                   
## [13] "ORF10, ORF11"               "ORF32, ORF33, ORF34"       
## [15] "NOIR_1"                     "NOIR_2"                    
## [17] "ORF24"                      "ORF64_1"
## [1] 18

Clustering statistics: Cluster number: 12

## Key: <cluster>
##     cluster                          gene        si        au        bp
##       <int>                        <char>     <num>     <num>     <num>
##  1:       1                          ORF1 1.0000000 1.0000000 1.0000000
##  2:       1                         ORF17 1.0000000 1.0000000 1.0000000
##  3:       1           ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
##  4:       1                         ORF31 1.0000000 1.0000000 1.0000000
##  5:       1                ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
##  6:       1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
##  7:       2                          ORF2 0.9984163 0.9994835 0.9913488
##  8:       2                         ORF40 0.9984163 0.9994835 0.9913488
##  9:       3                          ORF3 0.1234810 0.5986755 0.5152662
## 10:       3                          ORF9 0.1234810 0.5986755 0.5152662
## 11:       3                         ORF18 0.1234810 0.5986755 0.5152662
## 12:       3                  ORF28, ORF29 0.1234810 0.5986755 0.5152662
## 13:       3                         ORF37 0.1234810 0.5986755 0.5152662
## 14:       3                         ORF38 0.1234810 0.5986755 0.5152662
## 15:       3    ORF48, ORF49, ORF50, ORF51 0.1234810 0.5986755 0.5152662
## 16:       3                       ORF66_1 0.1234810 0.5986755 0.5152662
## 17:       4                          ORF4 0.9835030 0.9950607 0.9367211
## 18:       5            ORF7,  ORF6,  ORF5 0.2997682 0.6679639 0.6197278
## 19:       5                         ORF30 0.2997682 0.6679639 0.6197278
## 20:       5                         ORF63 0.2997682 0.6679639 0.6197278
## 21:       5                       ORF65_1 0.2997682 0.6679639 0.6197278
## 22:       6                          ORF8 0.8300888 0.9339235 0.8267064
## 23:       6           ORF12, ORF13, ORF14 0.8300888 0.9339235 0.8267064
## 24:       6                         ORF22 0.8300888 0.9339235 0.8267064
## 25:       6                         ORF23 0.8300888 0.9339235 0.8267064
## 26:       6           ORF27, ORF26, ORF25 0.8300888 0.9339235 0.8267064
## 27:       6  ORF37, ORF36, ORF35, ORF35.5 0.8300888 0.9339235 0.8267064
## 28:       6                         ORF36 0.8300888 0.9339235 0.8267064
## 29:       6                           CTO 0.8300888 0.9339235 0.8267064
## 30:       6            ORF41, ORF42, OF43 0.8300888 0.9339235 0.8267064
## 31:       6                         ORF44 0.8300888 0.9339235 0.8267064
## 32:       7                  ORF10, ORF11 0.9933681 0.9978948 0.9720753
## 33:       7           ORF32, ORF33, ORF34 0.9933681 0.9978948 0.9720753
## 34:       7                        NOIR_1 0.9933681 0.9978948 0.9720753
## 35:       7                        NOIR_2 0.9933681 0.9978948 0.9720753
## 36:       8    ORF18, ORF17, ORF16, ORF15 0.6634756 0.9263861 0.4587966
## 37:       8                         ORF19 0.6634756 0.9263861 0.4587966
## 38:       8                         ORF52 0.6634756 0.9263861 0.4587966
## 39:       8                  ORF53, ORF54 0.6634756 0.9263861 0.4587966
## 40:       8                  ORF57, ORF58 0.6634756 0.9263861 0.4587966
## 41:       8     ORF62, ORF61, ORF60,ORF59 0.6634756 0.9263861 0.4587966
## 42:       8           ORF71, ORF72, ORF73 0.6634756 0.9263861 0.4587966
## 43:       9                         ORF24 0.9969977 0.9993334 0.9533299
## 44:      10                         ORF39 0.1972185 0.6641499 0.5046373
## 45:      10                  ORF45, ORF46 0.1972185 0.6641499 0.5046373
## 46:      11                       ORF64_1 0.3578670 0.7264224 0.5906138
## 47:      12                  ORF69, ORF70 0.7907384 0.9441859 0.6350977
##     cluster                          gene        si        au        bp
##           se.si        se.au       se.bp          v          c       pchi
##           <num>        <num>       <num>      <num>      <num>      <num>
##  1: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  2: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  3: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  4: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  5: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  6: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  7: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
##  8: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
##  9: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 10: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 11: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 12: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 13: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 14: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 15: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 16: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 17: 0.004356308 0.0015792923 0.002805170 -2.0539348 0.52611717 0.07101361
## 18: 0.038198268 0.0281444577 0.005132608 -0.3695320 0.06476593 0.63603543
## 19: 0.038198268 0.0281444577 0.005132608 -0.3695320 0.06476593 0.63603543
## 20: 0.038198268 0.0281444577 0.005132608 -0.3695320 0.06476593 0.63603543
## 21: 0.038198268 0.0281444577 0.005132608 -0.3695320 0.06476593 0.63603543
## 22: 0.022308499 0.0112787217 0.004124539 -1.2234480 0.28221817 0.39334222
## 23: 0.022308499 0.0112787217 0.004124539 -1.2234480 0.28221817 0.39334222
## 24: 0.022308499 0.0112787217 0.004124539 -1.2234480 0.28221817 0.39334222
## 25: 0.022308499 0.0112787217 0.004124539 -1.2234480 0.28221817 0.39334222
## 26: 0.022308499 0.0112787217 0.004124539 -1.2234480 0.28221817 0.39334222
## 27: 0.022308499 0.0112787217 0.004124539 -1.2234480 0.28221817 0.39334222
## 28: 0.022308499 0.0112787217 0.004124539 -1.2234480 0.28221817 0.39334222
## 29: 0.022308499 0.0112787217 0.004124539 -1.2234480 0.28221817 0.39334222
## 30: 0.022308499 0.0112787217 0.004124539 -1.2234480 0.28221817 0.39334222
## 31: 0.022308499 0.0112787217 0.004124539 -1.2234480 0.28221817 0.39334222
## 32: 0.002536253 0.0009466593 0.001993169 -2.3870795 0.47487133 0.20691421
## 33: 0.002536253 0.0009466593 0.001993169 -2.3870795 0.47487133 0.20691421
## 34: 0.002536253 0.0009466593 0.001993169 -2.3870795 0.47487133 0.20691421
## 35: 0.002536253 0.0009466593 0.001993169 -2.3870795 0.47487133 0.20691421
## 36: 0.033546589 0.0110144449 0.005278204 -0.6729635 0.77642943 0.44948901
## 37: 0.033546589 0.0110144449 0.005278204 -0.6729635 0.77642943 0.44948901
## 38: 0.033546589 0.0110144449 0.005278204 -0.6729635 0.77642943 0.44948901
## 39: 0.033546589 0.0110144449 0.005278204 -0.6729635 0.77642943 0.44948901
## 40: 0.033546589 0.0110144449 0.005278204 -0.6729635 0.77642943 0.44948901
## 41: 0.033546589 0.0110144449 0.005278204 -0.6729635 0.77642943 0.44948901
## 42: 0.033546589 0.0110144449 0.005278204 -0.6729635 0.77642943 0.44948901
## 43: 0.001063096 0.0002821407 0.002535222 -2.4433858 0.76535080 0.33851817
## 44: 0.040087721 0.0279291195 0.005273401 -0.2177200 0.20609572 0.79095438
## 45: 0.040087721 0.0279291195 0.005273401 -0.2177200 0.20609572 0.79095438
## 46: 0.039008015 0.0256194980 0.005198635 -0.4155763 0.18645213 0.61297835
## 47: 0.023764101 0.0088428006 0.005150715 -0.9681515 0.62276603 0.47243662
##           se.si        se.au       se.bp          v          c       pchi

## [1] "ORF28, ORF29" "ORF66_1"
## [1] 2
##  [1] "ORF3"                         "ORF9"                        
##  [3] "ORF18"                        "ORF28, ORF29"                
##  [5] "ORF37"                        "ORF38"                       
##  [7] "ORF48, ORF49, ORF50, ORF51"   "ORF66_1"                     
##  [9] "ORF7,  ORF6,  ORF5"           "ORF30"                       
## [11] "ORF63"                        "ORF65_1"                     
## [13] "ORF8"                         "ORF12, ORF13, ORF14"         
## [15] "ORF22"                        "ORF23"                       
## [17] "ORF27, ORF26, ORF25"          "ORF37, ORF36, ORF35, ORF35.5"
## [19] "ORF36"                        "CTO"                         
## [21] "ORF41, ORF42, OF43"           "ORF44"                       
## [23] "ORF18, ORF17, ORF16, ORF15"   "ORF19"                       
## [25] "ORF52"                        "ORF53, ORF54"                
## [27] "ORF57, ORF58"                 "ORF62, ORF61, ORF60,ORF59"   
## [29] "ORF71, ORF72, ORF73"          "ORF39"                       
## [31] "ORF45, ORF46"                 "ORF64_1"                     
## [33] "ORF69, ORF70"
## [1] 33

Selected number of clusters: 12

## Key: <cluster>
##     cluster                          gene        si        au        bp
##       <int>                        <char>     <num>     <num>     <num>
##  1:       1                          ORF1 1.0000000 1.0000000 1.0000000
##  2:       1                         ORF17 1.0000000 1.0000000 1.0000000
##  3:       1           ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
##  4:       1                         ORF31 1.0000000 1.0000000 1.0000000
##  5:       1                ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
##  6:       1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
##  7:       2                          ORF2 0.9984163 0.9994835 0.9913488
##  8:       2                         ORF40 0.9984163 0.9994835 0.9913488
##  9:       3                          ORF3 0.1234810 0.5986755 0.5152662
## 10:       3                          ORF9 0.1234810 0.5986755 0.5152662
## 11:       3                         ORF18 0.1234810 0.5986755 0.5152662
## 12:       3                  ORF28, ORF29 0.1234810 0.5986755 0.5152662
## 13:       3                         ORF37 0.1234810 0.5986755 0.5152662
## 14:       3                         ORF38 0.1234810 0.5986755 0.5152662
## 15:       3    ORF48, ORF49, ORF50, ORF51 0.1234810 0.5986755 0.5152662
## 16:       3                       ORF66_1 0.1234810 0.5986755 0.5152662
## 17:       4                          ORF4 0.9835030 0.9950607 0.9367211
## 18:       5            ORF7,  ORF6,  ORF5 0.2997682 0.6679639 0.6197278
## 19:       5                         ORF30 0.2997682 0.6679639 0.6197278
## 20:       5                         ORF63 0.2997682 0.6679639 0.6197278
## 21:       5                       ORF65_1 0.2997682 0.6679639 0.6197278
## 22:       6                          ORF8 0.8300888 0.9339235 0.8267064
## 23:       6           ORF12, ORF13, ORF14 0.8300888 0.9339235 0.8267064
## 24:       6                         ORF22 0.8300888 0.9339235 0.8267064
## 25:       6                         ORF23 0.8300888 0.9339235 0.8267064
## 26:       6           ORF27, ORF26, ORF25 0.8300888 0.9339235 0.8267064
## 27:       6  ORF37, ORF36, ORF35, ORF35.5 0.8300888 0.9339235 0.8267064
## 28:       6                         ORF36 0.8300888 0.9339235 0.8267064
## 29:       6                           CTO 0.8300888 0.9339235 0.8267064
## 30:       6            ORF41, ORF42, OF43 0.8300888 0.9339235 0.8267064
## 31:       6                         ORF44 0.8300888 0.9339235 0.8267064
## 32:       7                  ORF10, ORF11 0.9933681 0.9978948 0.9720753
## 33:       7           ORF32, ORF33, ORF34 0.9933681 0.9978948 0.9720753
## 34:       7                        NOIR_1 0.9933681 0.9978948 0.9720753
## 35:       7                        NOIR_2 0.9933681 0.9978948 0.9720753
## 36:       8    ORF18, ORF17, ORF16, ORF15 0.6634756 0.9263861 0.4587966
## 37:       8                         ORF19 0.6634756 0.9263861 0.4587966
## 38:       8                         ORF52 0.6634756 0.9263861 0.4587966
## 39:       8                  ORF53, ORF54 0.6634756 0.9263861 0.4587966
## 40:       8                  ORF57, ORF58 0.6634756 0.9263861 0.4587966
## 41:       8     ORF62, ORF61, ORF60,ORF59 0.6634756 0.9263861 0.4587966
## 42:       8           ORF71, ORF72, ORF73 0.6634756 0.9263861 0.4587966
## 43:       9                         ORF24 0.9969977 0.9993334 0.9533299
## 44:      10                         ORF39 0.1972185 0.6641499 0.5046373
## 45:      10                  ORF45, ORF46 0.1972185 0.6641499 0.5046373
## 46:      11                       ORF64_1 0.3578670 0.7264224 0.5906138
## 47:      12                  ORF69, ORF70 0.7907384 0.9441859 0.6350977
##     cluster                          gene        si        au        bp
##           se.si        se.au       se.bp          v          c       pchi
##           <num>        <num>       <num>      <num>      <num>      <num>
##  1: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  2: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  3: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  4: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  5: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  6: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  7: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
##  8: 0.001174487 0.0004370967 0.001338253 -2.8307943 0.45057722 0.60441530
##  9: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 10: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 11: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 12: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 13: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 14: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 15: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 16: 0.037632624 0.0295733251 0.005270440 -0.1440981 0.10582218 0.93876278
## 17: 0.004356308 0.0015792923 0.002805170 -2.0539348 0.52611717 0.07101361
## 18: 0.038198268 0.0281444577 0.005132608 -0.3695320 0.06476593 0.63603543
## 19: 0.038198268 0.0281444577 0.005132608 -0.3695320 0.06476593 0.63603543
## 20: 0.038198268 0.0281444577 0.005132608 -0.3695320 0.06476593 0.63603543
## 21: 0.038198268 0.0281444577 0.005132608 -0.3695320 0.06476593 0.63603543
## 22: 0.022308499 0.0112787217 0.004124539 -1.2234480 0.28221817 0.39334222
## 23: 0.022308499 0.0112787217 0.004124539 -1.2234480 0.28221817 0.39334222
## 24: 0.022308499 0.0112787217 0.004124539 -1.2234480 0.28221817 0.39334222
## 25: 0.022308499 0.0112787217 0.004124539 -1.2234480 0.28221817 0.39334222
## 26: 0.022308499 0.0112787217 0.004124539 -1.2234480 0.28221817 0.39334222
## 27: 0.022308499 0.0112787217 0.004124539 -1.2234480 0.28221817 0.39334222
## 28: 0.022308499 0.0112787217 0.004124539 -1.2234480 0.28221817 0.39334222
## 29: 0.022308499 0.0112787217 0.004124539 -1.2234480 0.28221817 0.39334222
## 30: 0.022308499 0.0112787217 0.004124539 -1.2234480 0.28221817 0.39334222
## 31: 0.022308499 0.0112787217 0.004124539 -1.2234480 0.28221817 0.39334222
## 32: 0.002536253 0.0009466593 0.001993169 -2.3870795 0.47487133 0.20691421
## 33: 0.002536253 0.0009466593 0.001993169 -2.3870795 0.47487133 0.20691421
## 34: 0.002536253 0.0009466593 0.001993169 -2.3870795 0.47487133 0.20691421
## 35: 0.002536253 0.0009466593 0.001993169 -2.3870795 0.47487133 0.20691421
## 36: 0.033546589 0.0110144449 0.005278204 -0.6729635 0.77642943 0.44948901
## 37: 0.033546589 0.0110144449 0.005278204 -0.6729635 0.77642943 0.44948901
## 38: 0.033546589 0.0110144449 0.005278204 -0.6729635 0.77642943 0.44948901
## 39: 0.033546589 0.0110144449 0.005278204 -0.6729635 0.77642943 0.44948901
## 40: 0.033546589 0.0110144449 0.005278204 -0.6729635 0.77642943 0.44948901
## 41: 0.033546589 0.0110144449 0.005278204 -0.6729635 0.77642943 0.44948901
## 42: 0.033546589 0.0110144449 0.005278204 -0.6729635 0.77642943 0.44948901
## 43: 0.001063096 0.0002821407 0.002535222 -2.4433858 0.76535080 0.33851817
## 44: 0.040087721 0.0279291195 0.005273401 -0.2177200 0.20609572 0.79095438
## 45: 0.040087721 0.0279291195 0.005273401 -0.2177200 0.20609572 0.79095438
## 46: 0.039008015 0.0256194980 0.005198635 -0.4155763 0.18645213 0.61297835
## 47: 0.023764101 0.0088428006 0.005150715 -0.9681515 0.62276603 0.47243662
##           se.si        se.au       se.bp          v          c       pchi

## [1] "ORF28, ORF29" "ORF66_1"
## [1] 2
##  [1] "ORF3"                         "ORF9"                        
##  [3] "ORF18"                        "ORF28, ORF29"                
##  [5] "ORF37"                        "ORF38"                       
##  [7] "ORF48, ORF49, ORF50, ORF51"   "ORF66_1"                     
##  [9] "ORF7,  ORF6,  ORF5"           "ORF30"                       
## [11] "ORF63"                        "ORF65_1"                     
## [13] "ORF8"                         "ORF12, ORF13, ORF14"         
## [15] "ORF22"                        "ORF23"                       
## [17] "ORF27, ORF26, ORF25"          "ORF37, ORF36, ORF35, ORF35.5"
## [19] "ORF36"                        "CTO"                         
## [21] "ORF41, ORF42, OF43"           "ORF44"                       
## [23] "ORF18, ORF17, ORF16, ORF15"   "ORF19"                       
## [25] "ORF52"                        "ORF53, ORF54"                
## [27] "ORF57, ORF58"                 "ORF62, ORF61, ORF60,ORF59"   
## [29] "ORF71, ORF72, ORF73"          "ORF39"                       
## [31] "ORF45, ORF46"                 "ORF64_1"                     
## [33] "ORF69, ORF70"
## [1] 33

Remove genes from clusters ?

##  [1] "ORF3"                         "ORF9"                        
##  [3] "ORF18"                        "ORF28, ORF29"                
##  [5] "ORF37"                        "ORF38"                       
##  [7] "ORF48, ORF49, ORF50, ORF51"   "ORF66_1"                     
##  [9] "ORF7,  ORF6,  ORF5"           "ORF30"                       
## [11] "ORF63"                        "ORF65_1"                     
## [13] "ORF8"                         "ORF12, ORF13, ORF14"         
## [15] "ORF22"                        "ORF23"                       
## [17] "ORF27, ORF26, ORF25"          "ORF37, ORF36, ORF35, ORF35.5"
## [19] "ORF36"                        "CTO"                         
## [21] "ORF41, ORF42, OF43"           "ORF44"                       
## [23] "ORF18, ORF17, ORF16, ORF15"   "ORF19"                       
## [25] "ORF52"                        "ORF53, ORF54"                
## [27] "ORF57, ORF58"                 "ORF62, ORF61, ORF60,ORF59"   
## [29] "ORF71, ORF72, ORF73"          "ORF39"                       
## [31] "ORF45, ORF46"                 "ORF64_1"                     
## [33] "ORF69, ORF70"
## [1] 33
## No genes were removed from their corresponding clusters.
##     cluster     N
##       <int> <int>
##  1:       6    10
##  2:       3     8
##  3:       8     7
##  4:       1     6
##  5:       5     4
##  6:       7     4
##  7:       2     2
##  8:      10     2
##  9:       4     1
## 10:       9     1
## 11:      11     1
## 12:      12     1

Merge cluster stats

Assigning genes to clusters

Summarize and melt

Heatmaps

Normalized Expression

Expression delta ~ 6 hpi

Z-score of expression delta ~ 6 hpi

ORF kinetics, according to literature-based kinetic classes

Barplot of mean and SD

Figure 4 REVIEW - Mean and SD with linear connection

Mean and SD with loess function

Mean and SD with linear connection - Figure 4

Each replicate with loess

ORF kinetics, according to de-novo kinetic classes

Mean and SD with linear connection

Figure 5 REVIEW - Mean and SD with linear connection

Compare literature and de novo kinetic classes

NA shows the number of genes where the clustering did not yield an unambiguous result.

Combined Kinetic classes

De Novo Clusters

Literature clusters